* using log directory 'd:/Rcompile/CRANpkg/local/4.4/targeted.Rcheck' * using R version 4.4.3 (2025-02-28 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'targeted/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'targeted' version '0.6' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'targeted' can be installed ... OK * used C++ compiler: 'g++.exe (GCC) 13.3.0' * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [3s] OK * checking whether the package can be loaded with stated dependencies ... [3s] OK * checking whether the package can be unloaded cleanly ... [3s] OK * checking whether the namespace can be loaded with stated dependencies ... [3s] OK * checking whether the namespace can be unloaded cleanly ... [3s] OK * checking loading without being on the library search path ... [3s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [21s] OK * checking Rd files ... [2s] OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... [0s] OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compiled code ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [51s] ERROR Running examples in 'targeted-Ex.R' failed The error most likely occurred in: > ### Name: learner_xgboost > ### Title: Construct a learner > ### Aliases: learner_xgboost > > ### ** Examples > > n <- 1e3 > x1 <- rnorm(n, sd = 2) > x2 <- rnorm(n) > lp <- x2*x1 + cos(x1) > yb <- rbinom(n, 1, lava::expit(lp)) > y <- lp + rnorm(n, sd = 0.5**.5) > d0 <- data.frame(y, yb, x1, x2) > > # regression > lr <- learner_xgboost(y ~ x1 + x2, nrounds = 5) > lr$estimate(d0) Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized), : Passed unrecognized parameters: verbose. This warning will become an error in a future version. Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", : Parameter 'data' has been renamed to 'x'. This warning will become an error in a future version. Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", : Parameter 'eta' has been renamed to 'learning_rate'. This warning will become an error in a future version. Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", : Parameter 'lambda' has been renamed to 'reg_lambda'. This warning will become an error in a future version. Error in (function (x, y, objective = NULL, nrounds = 100L, max_depth = NULL, : argument "y" is missing, with no default Calls: ... -> process.y.margin.and.objective -> NROW Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... [32s] ERROR Running 'tinytest.R' [32s] Running the tests in 'tests/tinytest.R' failed. Complete output: > > if (requireNamespace("tinytest", quietly = TRUE)) { + + ## future::plan("sequential") + Sys.setenv("OMP_THREAD_LIMIT" = 2) + options(Ncpus = 1) + data.table::setDTthreads(1) + + tinytest::test_package("targeted") + } test_cate.R................... 0 tests test_cate.R................... 0 tests test_cate.R................... 0 tests test_cate.R................... 0 tests test_cate.R................... 0 tests test_cate.R................... 0 tests test_cate.R................... 0 tests test_cate.R................... 0 tests test_cate.R................... 0 tests test_cate.R................... 1 tests OK test_cate.R................... 2 tests OK test_cate.R................... 2 tests OK test_cate.R................... 11 tests OK test_cate.R................... 11 tests OK test_cate.R................... 23 tests OK test_cate.R................... 23 tests OK test_cate.R................... 27 tests OK test_cate.R................... 27 tests OK test_cate.R................... 27 tests OK test_cate.R................... 31 tests OK test_cate.R................... 31 tests OK test_cate.R................... 31 tests OK test_cate.R................... 31 tests OK test_cate.R................... 31 tests OK test_cate.R................... 31 tests OK test_cate.R................... 31 tests OK test_cate.R................... 31 tests OK test_cate.R................... 31 tests OK test_cate.R................... 35 tests OK test_cate.R................... 35 tests OK test_cate.R................... 36 tests OK 8.2s test_cumhaz.R................. 0 tests test_cumhaz.R................. 0 tests test_cumhaz.R................. 0 tests test_cumhaz.R................. 0 tests test_cumhaz.R................. 0 tests test_cumhaz.R................. 0 tests test_cumhaz.R................. 0 tests test_cumhaz.R................. 0 tests test_cumhaz.R................. 0 tests test_cumhaz.R................. 0 tests test_cumhaz.R................. 0 tests test_cumhaz.R................. 0 tests test_cumhaz.R................. 0 tests test_cumhaz.R................. 0 tests test_cumhaz.R................. 0 tests test_cumhaz.R................. 0 tests test_cumhaz.R................. 5 tests OK test_cumhaz.R................. 5 tests OK test_cumhaz.R................. 5 tests OK test_cumhaz.R................. 5 tests OK test_cumhaz.R................. 5 tests OK test_cumhaz.R................. 6 tests OK test_cumhaz.R................. 6 tests OK test_cumhaz.R................. 11 tests OK test_cumhaz.R................. 11 tests OK test_cumhaz.R................. 11 tests OK test_cumhaz.R................. 11 tests OK test_cumhaz.R................. 11 tests OK test_cumhaz.R................. 11 tests OK test_cumhaz.R................. 11 tests OK test_cumhaz.R................. 12 tests OK test_cumhaz.R................. 12 tests OK test_cumhaz.R................. 17 tests OK test_cumhaz.R................. 17 tests OK test_cumhaz.R................. 22 tests OK test_cumhaz.R................. 22 tests OK test_cumhaz.R................. 22 tests OK test_cumhaz.R................. 27 tests OK test_cumhaz.R................. 27 tests OK test_cumhaz.R................. 27 tests OK test_cumhaz.R................. 28 tests OK test_cumhaz.R................. 28 tests OK test_cumhaz.R................. 28 tests OK test_cumhaz.R................. 28 tests OK test_cumhaz.R................. 29 tests OK test_cumhaz.R................. 34 tests OK test_cumhaz.R................. 34 tests OK test_cumhaz.R................. 34 tests OK test_cumhaz.R................. 34 tests OK test_cumhaz.R................. 34 tests OK test_cumhaz.R................. 35 tests OK test_cumhaz.R................. 35 tests OK test_cumhaz.R................. 40 tests OK test_cumhaz.R................. 41 tests OK test_cumhaz.R................. 41 tests OK test_cumhaz.R................. 41 tests OK test_cumhaz.R................. 41 tests OK test_cumhaz.R................. 41 tests OK test_cumhaz.R................. 42 tests OK test_cumhaz.R................. 42 tests OK test_cumhaz.R................. 42 tests OK test_cumhaz.R................. 43 tests OK test_cumhaz.R................. 43 tests OK test_cumhaz.R................. 43 tests OK test_cumhaz.R................. 44 tests OK test_cumhaz.R................. 44 tests OK test_cumhaz.R................. 44 tests OK test_cumhaz.R................. 44 tests OK test_cumhaz.R................. 45 tests OK test_cumhaz.R................. 45 tests OK test_cumhaz.R................. 46 tests OK test_cumhaz.R................. 46 tests OK test_cumhaz.R................. 51 tests OK test_cumhaz.R................. 51 tests OK test_cumhaz.R................. 51 tests OK test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 56 tests OK Attaching package: 'survival' The following object is masked from 'package:future': cluster test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 56 tests OK test_cumhaz.R................. 63 tests OK test_cumhaz.R................. 63 tests OK test_cumhaz.R................. 70 tests OK test_cumhaz.R................. 70 tests OK test_cumhaz.R................. 77 tests OK 8.7s test_design.R................. 0 tests test_design.R................. 0 tests test_design.R................. 0 tests test_design.R................. 0 tests test_design.R................. 0 tests test_design.R................. 11 tests OK test_design.R................. 11 tests OK test_design.R................. 14 tests OK test_design.R................. 14 tests OK test_design.R................. 30 tests OK test_design.R................. 30 tests OK test_design.R................. 30 tests OK test_design.R................. 36 tests OK test_design.R................. 36 tests OK test_design.R................. 38 tests OK test_design.R................. 38 tests OK test_design.R................. 48 tests OK test_design.R................. 48 tests OK test_design.R................. 55 tests OK test_design.R................. 55 tests OK test_design.R................. 62 tests OK test_design.R................. 62 tests OK test_design.R................. 64 tests OK 0.2s test_expand_list.R............ 0 tests test_expand_list.R............ 0 tests test_expand_list.R............ 0 tests test_expand_list.R............ 18 tests OK 9ms test_intersection_sw.R........ 0 tests test_intersection_sw.R........ 0 tests test_intersection_sw.R........ 0 tests test_intersection_sw.R........ 0 tests test_intersection_sw.R........ 0 tests test_intersection_sw.R........ 0 tests test_intersection_sw.R........ 0 tests test_intersection_sw.R........ 0 tests test_intersection_sw.R........ 0 tests 11ms test_intsurv.R................ 0 tests test_intsurv.R................ 0 tests test_intsurv.R................ 0 tests test_intsurv.R................ 0 tests test_intsurv.R................ 0 tests test_intsurv.R................ 0 tests test_intsurv.R................ 0 tests test_intsurv.R................ 0 tests test_intsurv.R................ 0 tests test_intsurv.R................ 0 tests test_intsurv.R................ 0 tests test_intsurv.R................ 0 tests test_intsurv.R................ 0 tests test_intsurv.R................ 0 tests test_intsurv.R................ 0 tests test_intsurv.R................ 0 tests test_intsurv.R................ 0 tests test_intsurv.R................ 0 tests test_intsurv.R................ 0 tests test_intsurv.R................ 1 tests OK test_intsurv.R................ 2 tests OK test_intsurv.R................ 2 tests OK test_intsurv.R................ 2 tests OK test_intsurv.R................ 2 tests OK test_intsurv.R................ 3 tests OK 35ms test_learner.R................ 0 tests test_learner.R................ 0 tests test_learner.R................ 0 tests test_learner.R................ 0 tests test_learner.R................ 0 tests test_learner.R................ 0 tests test_learner.R................ 0 tests test_learner.R................ 5 tests OK test_learner.R................ 5 tests OK test_learner.R................ 13 tests OK test_learner.R................ 13 tests OK test_learner.R................ 17 tests OK test_learner.R................ 17 tests OK test_learner.R................ 24 tests OK test_learner.R................ 24 tests OK test_learner.R................ 28 tests OK test_learner.R................ 28 tests OK test_learner.R................ 32 tests OK test_learner.R................ 32 tests OK test_learner.R................ 43 tests OK test_learner.R................ 43 tests OK test_learner.R................ 45 tests OK test_learner.R................ 45 tests OK test_learner.R................ 51 tests OK 0.8s test_learner_expand_grid.R.... 0 tests test_learner_expand_grid.R.... 1 tests OK test_learner_expand_grid.R.... 1 tests OK test_learner_expand_grid.R.... 2 tests OK test_learner_expand_grid.R.... 2 tests OK test_learner_expand_grid.R.... 3 tests OK test_learner_expand_grid.R.... 3 tests OK test_learner_expand_grid.R.... 4 tests OK test_learner_expand_grid.R.... 4 tests OK test_learner_expand_grid.R.... 4 tests OK test_learner_expand_grid.R.... 5 tests OK test_learner_expand_grid.R.... 6 tests OK test_learner_expand_grid.R.... 6 tests OK test_learner_expand_grid.R.... 7 tests OK test_learner_expand_grid.R.... 8 tests OK 53ms test_learner_glm.R............ 0 tests test_learner_glm.R............ 0 tests test_learner_glm.R............ 0 tests test_learner_glm.R............ 0 tests test_learner_glm.R............ 0 tests test_learner_glm.R............ 0 tests test_learner_glm.R............ 8 tests OK 0.1s test_learner_glmnet.R......... 0 tests test_learner_glmnet.R......... 0 tests test_learner_glmnet.R......... 0 tests test_learner_glmnet.R......... 0 tests test_learner_glmnet.R......... 0 tests test_learner_glmnet.R......... 0 tests test_learner_glmnet.R......... 8 tests OK 3.4s test_learner_grf.R............ 0 tests test_learner_grf.R............ 0 tests test_learner_grf.R............ 0 tests test_learner_grf.R............ 0 tests test_learner_grf.R............ 0 tests test_learner_grf.R............ 0 tests test_learner_grf.R............ 0 tests test_learner_grf.R............ 1 tests OK test_learner_grf.R............ 2 tests OK test_learner_grf.R............ 2 tests OK test_learner_grf.R............ 2 tests OK test_learner_grf.R............ 3 tests OK test_learner_grf.R............ 3 tests OK test_learner_grf.R............ 4 tests OK test_learner_grf.R............ 5 tests OK test_learner_grf.R............ 5 tests OK test_learner_grf.R............ 6 tests OK test_learner_grf.R............ 7 tests OK test_learner_grf.R............ 7 tests OK test_learner_grf.R............ 7 tests OK test_learner_grf.R............ 7 tests OK test_learner_grf.R............ 8 tests OK test_learner_grf.R............ 9 tests OK test_learner_grf.R............ 9 tests OK test_learner_grf.R............ 9 tests OK test_learner_grf.R............ 9 tests OK test_learner_grf.R............ 10 tests OK test_learner_grf.R............ 10 tests OK test_learner_grf.R............ 10 tests OK test_learner_grf.R............ 10 tests OK 3.2s test_learner_hal.R............ 0 tests test_learner_hal.R............ 0 tests test_learner_hal.R............ 0 tests test_learner_hal.R............ 0 tests test_learner_hal.R............ 3 tests OK 0.7s test_learner_isoreg.R......... 0 tests test_learner_isoreg.R......... 0 tests test_learner_isoreg.R......... 0 tests test_learner_isoreg.R......... 0 tests test_learner_isoreg.R......... 0 tests test_learner_isoreg.R......... 0 tests test_learner_isoreg.R......... 0 tests test_learner_isoreg.R......... 0 tests test_learner_isoreg.R......... 0 tests test_learner_isoreg.R......... 1 tests OK test_learner_isoreg.R......... 2 tests OK test_learner_isoreg.R......... 2 tests OK test_learner_isoreg.R......... 3 tests OK 19ms test_learner_mars.R........... 0 tests test_learner_mars.R........... 0 tests test_learner_mars.R........... 0 tests test_learner_mars.R........... 0 tests test_learner_mars.R........... 0 tests test_learner_mars.R........... 0 tests test_learner_mars.R........... 5 tests OK 0.3s test_learner_naivebayes.R..... 0 tests test_learner_naivebayes.R..... 0 tests test_learner_naivebayes.R..... 0 tests test_learner_naivebayes.R..... 0 tests test_learner_naivebayes.R..... 0 tests test_learner_naivebayes.R..... 0 tests test_learner_naivebayes.R..... 1 tests OK test_learner_naivebayes.R..... 2 tests OK test_learner_naivebayes.R..... 2 tests OK test_learner_naivebayes.R..... 2 tests OK test_learner_naivebayes.R..... 2 tests OK test_learner_naivebayes.R..... 3 tests OK test_learner_naivebayes.R..... 4 tests OK test_learner_naivebayes.R..... 5 tests OK test_learner_naivebayes.R..... 5 tests OK test_learner_naivebayes.R..... 5 tests OK test_learner_naivebayes.R..... 6 tests OK test_learner_naivebayes.R..... 7 tests OK test_learner_naivebayes.R..... 7 tests OK test_learner_naivebayes.R..... 7 tests OK test_learner_naivebayes.R..... 7 tests OK test_learner_naivebayes.R..... 7 tests OK test_learner_naivebayes.R..... 7 tests OK test_learner_naivebayes.R..... 8 tests OK test_learner_naivebayes.R..... 8 tests OK test_learner_naivebayes.R..... 8 tests OK test_learner_naivebayes.R..... 9 tests OK test_learner_naivebayes.R..... 9 tests OK test_learner_naivebayes.R..... 9 tests OK test_learner_naivebayes.R..... 9 tests OK test_learner_naivebayes.R..... 9 tests OK test_learner_naivebayes.R..... 9 tests OK test_learner_naivebayes.R..... 9 tests OK test_learner_naivebayes.R..... 10 tests OK 0.6s test_learner_sl.R............. 0 tests test_learner_sl.R............. 0 tests test_learner_sl.R............. 0 tests test_learner_sl.R............. 0 tests test_learner_sl.R............. 5 tests OK 1.1s test_learner_stratify.R....... 0 tests test_learner_stratify.R....... 0 tests test_learner_stratify.R....... 0 tests test_learner_stratify.R....... 3 tests OK test_learner_stratify.R....... 3 tests OK test_learner_stratify.R....... 5 tests OK 0.1s test_learner_svm.R............ 0 tests test_learner_svm.R............ 0 tests test_learner_svm.R............ 0 tests test_learner_svm.R............ 0 tests test_learner_svm.R............ 0 tests test_learner_svm.R............ 1 tests OK test_learner_svm.R............ 2 tests OK test_learner_svm.R............ 2 tests OK test_learner_svm.R............ 2 tests OK test_learner_svm.R............ 2 tests OK test_learner_svm.R............ 2 tests OK test_learner_svm.R............ 2 tests OK test_learner_svm.R............ 2 tests OK test_learner_svm.R............ 3 tests OK test_learner_svm.R............ 3 tests OK test_learner_svm.R............ 3 tests OK test_learner_svm.R............ 4 tests OK test_learner_svm.R............ 5 tests OK test_learner_svm.R............ 5 tests OK test_learner_svm.R............ 5 tests OK test_learner_svm.R............ 6 tests OK test_learner_svm.R............ 7 tests OK test_learner_svm.R............ 8 tests OK test_learner_svm.R............ 8 tests OK test_learner_svm.R............ 9 tests OK test_learner_svm.R............ 9 tests OK test_learner_svm.R............ 9 tests OK test_learner_svm.R............ 10 tests OK 0.9s test_learner_xgboost.R........ 0 tests test_learner_xgboost.R........ 0 tests test_learner_xgboost.R........ 0 tests test_learner_xgboost.R........ 0 tests Error in (function (x, y, objective = NULL, nrounds = 100L, max_depth = NULL, : argument "y" is missing, with no default Calls: ... -> process.y.margin.and.objective -> NROW In addition: Warning messages: 1: In throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized), : Passed unrecognized parameters: verbose. This warning will become an error in a future version. 2: In throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", : Parameter 'data' has been renamed to 'x'. This warning will become an error in a future version. 3: In throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", : Parameter 'eta' has been renamed to 'learning_rate'. This warning will become an error in a future version. 4: In throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", : Parameter 'lambda' has been renamed to 'reg_lambda'. This warning will become an error in a future version. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [20s] ERROR Error(s) in re-building vignettes: --- re-building 'predictionclass.Rmd' using rmarkdown Quitting from predictionclass.Rmd:143-145 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! argument "y" is missing, with no default --- Backtrace: ▆ 1. └─lr_xgboost$estimate(data = pbc) 2. └─private$fitfun(data, ...) 3. ├─base::structure(do.call(private$init.estimate, args), design = summary(xx)) 4. ├─base::do.call(private$init.estimate, args) 5. └─targeted (local) ``(...) 6. ├─base::do.call(...) 7. └─xgboost (local) ``(...) 8. └─xgboost:::process.y.margin.and.objective(...) 9. └─base::NROW(y) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'predictionclass.Rmd' failed with diagnostics: argument "y" is missing, with no default --- failed re-building 'predictionclass.Rmd' --- re-building 'riskregression.Rmd' using rmarkdown --- finished re-building 'riskregression.Rmd' SUMMARY: processing the following file failed: 'predictionclass.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [20s] OK * checking HTML version of manual ... [13s] OK * DONE Status: 3 ERRORs